Protective Instincts
by MandyK
Summary: New trading partners aren't always what they seem, as Sheppard finds out to his detriment. Can he prevent disaster from happening?
1. Chapter 1

**Protective Instincts part one.**

**Prologue.**

The weather outside was stormy; the wind hurled rain against the windows, but inside Councillor Jacq'an's rooms it was comfortable, a haven against the inclement weather. A large fire burned in the hearth, amply warming the room, and the two men sat in comfortable armchairs one on each side of the fireplace, facing each other. They sipped at the locally produced spirit that filled their glasses as they conversed.

"And you are sure they will come here?" questioned the Councillor, inhaling the herbal fragrance of his drink.

"I am only surprised they haven't been here already," replied Commander Cowen of the Genii.

"And what will we receive for performing this – service on your behalf?"

"Preferential trading status with the Genii. And protection from the Wraith once we have perfected our weapon, of course." Cowen assured the councillor, sipping from his own glass.

"Of course," echoed Jaq'an. There was a pause while the Councillor considered his reply. Eventually he looked up with a calculating smile and said, "It will be a pleasure to assist the Genii in this matter. As you know, we Suventans consider ourselves something of experts with this kind of ...persuasion. In fact, we have just developed a new device for providing the kind of control you are looking for, and have been searching for a subject upon whom to test it."

"Then Major Sheppard will be your first success." Cowen raised his glass. Jaq'an followed suit.

"To co-operation," toasted Cowen.

"Indeed," responded the Councillor. The two men touched glasses, then drank deeply to seal the agreement.

oOo

Dr Elizabeth Weir paced anxiously at the foot of the ramp to the Stargate as she waited for the return of Major Sheppard. Her mouth was dry, and her stomach was knotted with anxiety, because she didn't know what she would be getting back. She had sent SGA-1 on a simple trading mission, but it had been doomed from the start. The Suventans weren't interested in trading, except for one thing –John Sheppard. The team hadn't realised the duplicity of the Suventans until they had walked through the Stargate when they had been quickly surrounded and disarmed without a single shot being fired.

Dr. Weir had worked tirelessly to secure their release, and her years as a negotiator on Earth had paid off when finally Ford, Teyla and McKay had been returned. Battered, bruised and the worse for wear, but safe. Not so Major Sheppard, and it had become apparent that he was the one they had really wanted from the start.

The mission debriefing had been held in the infirmary where the three remaining members of the team were resting and recovering from their ordeal. Teyla had had dealings with the Suventans in the past, though her contact with them was infrequent, and she had not known them well. She certainly had not known of their close trading links with the Genii, but continued to feel guilty that her recommendations were what had put the Major in harms way.

It seemed that they had been separated immediately; the Major had been missing from the very beginning, although the three couldn't say that their stay had been a pleasant one. Dr. McKay's persistent questions about the whereabouts of the Major and his wellbeing had resulted in a beating that had left him with a concussion severe enough to keep him as a guest in the infirmary for a while longer. That had been two days ago, and there was still no sign of the Major.

While Ford, Teyla and McKay were recovering, Elizabeth had continued to bargain for Sheppard's release, and then suddenly, when it had seemed hopeless, the Suventans had agreed to return him. The price they had set was steep, but not as high as she had imagined, and now here she was, waiting to welcome him back.

The gate came to life, and her heart rate accelerated. Beside her, she felt Dr. Beckett tense in anticipation, neither of them knowing quite what to expect. She had known that John was going to look rough when he finally did arrive home, but still… the first sight of him took her breath away. She heard Beckett take a breath in consternation .Teyla and Ford were virtually holding the Major up as they came through. They had insisted on being part of the retrieval team, despite their still healing bruises: McKay had been most vociferous in his protests when Carson had told him he couldn't go, as his concussion was severe enough for the doctor to want to observe him for a while longer.

Elizabeth tried to school her expression so that the shock she felt on seeing Sheppard for the first time wasn't evident, but she knew she had been only partially successful. Gone was the cheerful, confident, happy-go-lucky expression he'd had as he stepped through the event horizon all those days ago. Instead, the man standing in front of her might almost have been a stranger. His face was covered in dried blood and ground in dirt, one eye partially swollen closed. His hair was sticky and filthy, not the ebullient finger-in-the-socket style he usually had; instead, matted and unkempt, more dried blood evident in its strands. But it was his eyes that almost were her undoing. The expression in them was haunted, devoid of humour, and was that-fear? His face was gaunt and shadowed, cheeks hollow: his clothing ripped and dirty, and God alone knew what the torn uniform was concealing.

She went forward, words of welcome tripping out of her mouth, raising a hand to touch his face in a gesture of caring, but he flinched back involuntarily, and so she allowed her hand to drop, gesture incomplete. It was at this point that she realised that his wrists were still bound.

"Why is he restrained?" she demanded more harshly than she had intended.

"The Major won't let us take them off," replied Ford expressionlessly, obviously as unhappy about it as she was.

"What?" she said incredulously. "Get them off him, now."

"Please…don't take them off." It was the first thing John had said. His voice sounded hoarse, as if from not enough use, or maybe too much. Tears pricked at the back of Elizabeth's eyes, and she told herself sternly to pull herself together, not to go there, not now, not when she was in full view of everyone in the control room.

"Why?" she began, when Beckett decided to take part in the conversation. He had noticed that Sheppard was barely able to hold himself upright, and that standing there in the control room, everyone gawping at him wasn't helping.

"They can stay for now," he said sharply. Then he gently took hold of John's arm, assisting him to the waiting gurney. "C'mon, lad, let's get you to the infirmary –"

"No!" The vehemence in John's voice took them all by surprise.

"No," repeated the Major more quietly. "Not the infirmary. Please. I want you to take me to the brig."

There was a stunned silence. Elizabeth was the first to recover.

"John," she said quietly, "We've only just got you out of a prison. The last thing you need is to go to another one. Besides, you're hurt. Let us take you to the infirmary where Carson can – "

"Beckett can see to me in the brig just as well," interrupted the Major. "Put a mattress, or something in there if you want, just – just I can't be loose right now."

Elizabeth looked at him again, and saw the fear was back, lurking in his eyes.

"Please, " he asked, putting a filthy hand on her arm, "Please, I can't trust myself, you shouldn't trust me, not now." He stopped.

"Very well," she acquiesced, "But only as a temporary measure." She nodded to Beckett, who didn't look happy, but just nodded.

The group made its way to the brig, where a mattress had been placed per Dr.Weir's instructions. There was a tension evident in the Major that could be felt by those supporting him, but they felt him relax as he was enclosed by the cell.

"Turn on the shield," he said hoarsely.

Elizabeth nodded, and once Beckett was inside with John, Ford complied. Sheppard lay down gratefully against the pillows.

"Ok, son, let's have a look at you," said Beckett approaching him. "Then maybe you can tell me why we're here and not in the infirmary." He turned to look at Elizabeth, Teyla and Ford, along with other assorted members of soldiery who had drawn guard duty that day.

"D'you think we can have a bit of privacy here?" he asked pointedly. A weak grip on his arm caused him to look down.

"Don't let them go too far away," whispered an exhausted Sheppard.

"Don't worry, Major, Ford and Teyla will stay within earshot. I just want to have a quick look at you, then we can have that wee chat."

Elizabeth came over to say goodbye. John had his eyes closed. She looked at Beckett. "I'll be in my office when you're done," she said. "Take care of him," and she was gone.

TBC


	2. Chapter 2

PROTECTIVE INSTINCTS part two

**A/N If Sheppard appears confused in this part, that's because he is. I wanted to give the impression of someone's mind being slowly taken over...**

**And thank you everyone for the fantastic reveiws. It keeps the bunnies happy, and I'm writing...**

Dr. Weir was sitting in her office ostensibly going through some reports, but in reality woolgathering when Beckett came in. His whole demeanour was one of anger, though he was doing his best to hold it in.

"How is Major Sheppard?" she asked, gesturing for Beckett to sit. He complied, but took a moment before answering.

"The Major is dehydrated and suffering the effects of being held by hostiles whose only intent seems to have been to hurt him as much as they could. I can't tell too much in the brig, he needs X-rays and a thorough going over, but he's hurting. I've given him what I can for now, he'd only have painkillers, and mild ones at that, but I would really like to get him to the infirmary as soon as possible."

"Has he said anything about why he wants to be confined?"

"No, but underneath all the physical damage there's…something else. I tried to get him to talk to me, but he just clammed up. You know how he can be."

Elizabeth knew exactly how he could be.

"Well, we can't keep him in there for ever, sooner or later he'll have to explain himself. Would a chat with Dr. Heightmeyer help?"

Beckett sighed. "I thought of that," he admitted, "But I think what's needed now is for the Major to rest and get some fluids inside him. Then we can talk psychology. Major Sheppard is – er- resistant to analysis at the best of times."

Elizabeth nodded. "Well, keep an eye on him, and keep me informed."

Beckett agreed, then left. He had some of Sheppard's blood work he wanted to examine.

oOo

Major Sheppard lay on the cot in the Brig, one arm over his face, shielding his eyes from the lights which were too bright. Carson had finally done with him and had left, promising to come back later, extracting a promise in return that John would sleep. John was desperate to sleep; he'd had far too little of it in the past few days, but despite his best efforts, that blissful state continued to elude him.

He told himself the lights were too bright, and the tug in his left hand from the IV that Beckett had insisted he had was annoying, but it wasn't really these small irritations that were stopping him from dropping off. If he was really honest with himself, he was too afraid to sleep.

He shifted restlessly, feeling the aches and pains from his abused body. They were bearable now that the Doc had filled him full of painkillers, but they were still there. Beckett had wanted John to have the really strong stuff, the oblivion – inducing happy meds, but the Major had been adamant in his refusal. He needed the pain as long as it wasn't debilitating. A little pain kept him sharp.

He shifted restlessly again. Then there were the voices. Just on the edge of his hearing, so he felt as if he had to constantly strain to hear what they were saying. A susurration of noise like a hundred people all whispering at once. He had a feeling the voices wanted him to do something, something he wouldn't normally do, and he was resisting. That was why he was afraid to sleep, afraid to be sedated. He didn't know what would happen if he let go. And that was why he needed to be confined securely. Even John Sheppard couldn't stay awake for ever.

The Major knew that Elizabeth and Beckett wanted him to talk, to tell them why, but he wasn't ready to face it yet, not ready to acknowledge the violation that Jaq'an and the others on that planet had done to him.

God, he needed to SLEEP!

He began to feel an urge to move. The compulsion grew, he resisted. The voices grew louder, somehow telling him to move, to get out. He shifted again. And then again. Finally, he sat up, carefully swinging his legs over the edge of the cot, planting his elbows on his knees, and burrowing his face into his hands. He was aware Ford was watching him, concerned, but he ignored him. The voices were louder, pulsing inside his head, back and forth, ebb and flow. He pressed his hands against his temples, as if trying to block it out, or hold it in. Louder. They were getting louder, like bats beating around the inside of his skull.

"Goddammit! Shut up!" he yelled.

"Sir?" From Ford. "Major? Are you alright?"

Sheppard stood unsteadily, and began to pace, the IV dragged out of his hand by his restless motion, blood dripping onto the floor unnoticed as he limped around the cell. He had to get out, he had to get away, somewhere quiet, somewhere the voices wouldn't find him, somewhere he could think. He felt as if the walls of the cell, open as they were, were closing in on him. The lights pulsed in time with the voices, and now the whispering brought pain. White hot needles, stabbing, drilling into his skull.

Out. He had to get out. The pacing stopped. '_Out'_ whispered the voices, '_outoutoutout'_. Now he couldn't bear to be confined, not one moment longer.He began to hurl himself against the bars, thrown back by the forcefield he had insisted upon himself, staggering up to hurl himself at the bars again, and again…

Appalled, Ford hit the panic button shouting for Beckett and a medical team…

oOo

Beckett was back in Dr. Weir's office, updating her on the major's condition.

"I found something in Major Sheppard's blood sample," he said. "He has exceptionally high levels of adrenalin circulating. Something is stressing him much more than usual."

"Doctor, he's just been held captive and tortured. I would say that would increase his stress levels."

"No, I've taken that into account. This is something else." He sighed , "He really needs to be in the infirmary. Levels this high could indicate a malfunction of his adrenal glands, or something else that I haven't even begun to contemplate yet."

Elizabeth was about to answer when Ford's voice crackled over their intercoms. He sounded strained, urgent.

"We need a medical team to the brig!" he shouted.

"Crap!" swore Beckett as he headed out at a run.

Elizabeth followed closely behind. "Meet you in the brig!" she called after his retreating figure.

As Dr. Weir entered the holding area, she could hear Ford talking to the Major.

"Sir, Major, are you alright? Sir, you should stop." Ford almost sounded as if he was begging Sheppard to stop.

She came to an abrupt halt, taking in the scene before her. Major Sheppard was doggedly hurling himself at the bars of the cell, a look of desperation on his face. A second later, and Beckett had come to a skidding stop beside her, having called at the infirmary on the way over to collect his emergency kit. He was accompanied by Teyla and a med team. Sheppard was muttering incoherently to himself.

"Bloody hell," murmured Beckett. "He shouldn't be able to stand up let alone hurl himself around like that, the state he's in." he moved closer to the bars, Elizabeth right behind him.

"Major!" he rapped out sharply. "What do you think you're doing?"

The peremptory tone of his voice brought Sheppard out of his fugue. "Huh?" he asked, vague.

Beckett took in the state of the man in front of him. "Ah said, what do you think you're doing? You should be resting."

"I have to get out, they want me out. Please, Doc, don't let me…" he paled as a spike of pain drove through his head. He shifted restlessly, poised as if to flee. "They want… they want... I don't know what they WANT!.." He began pacing again.

"Who? Who wants something?" from Elizabeth.

"I don't know…the voices, the voices in my head…they keep whispering, they don't stop." He looked at Beckett, almost pleading. "You can make them stop doc, please…" He began the pacing again, but at least he wasn't throwing himself at the bars any more.

Beckett turned to Elizabeth who was looking on, horrified.

"I'm going to have to sedate him. He canna carry on like this, but I'll have to get in there to do it. Just give me a minute to prepare what I need."

Weir nodded, her gaze fixed on the man moving raggedly around the cell. "Whatever you need. Do it."

Teyla moved to the bars, distressed at seeing the Major the way he was.

"Major Sheppard?" she asked.

"Teyla?" he looked at her vaguely.

"Major, you must stop."

"Can't. If I stop, it gets louder."

"What gets louder?"

"The whispering, and if I ignore it, it hurts, I don't want it to hurt anymore." He pressed his hands to his head again, wincing. "I can't let them win."

"Who is it, Major? Who is doing this?"

"I…don't know…" he stopped., his voice getting quieter, almost back to muttering. "The whispering," he said conspiratorially, "It doesn't stop, please, make it stop, they're getting louder., I can't think straight, I need to be able to think…"

By this time, Beckett had loaded his syringe, and was ready at the entrance. Ford opened the door. Sheppard's head swung up sharply.

"What are you doing?" there was real fear in is voice. "Don't open it! If you open that door, I won't be able to help myself!"

"It's ok, John," said Beckett soothingly. "Ford's just letting me in to help you. He'll stay right there outside the door. You won't be able to go anywhere."

"Don't!" Sheppard was almost pleading.

Beckett nodded at Ford who started to open the cell. With a strangled cry, Sheppard tried to get out. Sheppard was working on adrenalin and desperation, while Ford was afraid of hurting his CO further. The Major was winning by dint of repeatedly pushing against the lieutenant and for a few comedic moments there was chaos as Beckett tried to get in, Ford tried to hold Sheppard back, and Sheppard fought to get out. Then there was a high- pitched whine, a bright blue flash, and Sheppard dropped.

Beckett whirled to see Teyla standing with a Wraith stunner held up. She met his shocked gaze squarely. "Someone had to stop him," she said, "Before he caused himself more harm."

Swallowing, Beckett reminded himself never to get on Teyla's bad side. "Right," he said. Help me to get him to the infirmary."

TBC


	3. Chapter 3

PROTECTIVE INSTINCTS part three,

**A/N Wow, all these wonderful reviews have put me in an extremely good mood. My family thank you all very much,(and so do I). Its truly wonderful to get such glowing reviews from people whose fic I look up to.**

**And now...a whumping we will go. Warning, bad things happen to Shep in this part.**

Major Sheppard gradually became aware of beeping noises and faint voices. The sounds were familiar enough he knew he was in the infirmary. _Crap,_ he thought. _Not again._ He was aware of the pins and needles feeling he got after being shot with a wraith stunner. _What the hell happened?_ he asked himself, and tried to raise his hand to rub at the headache nestled behind his eyes, only to find his hand wouldn't move. He opened his eyes, blinking against the bright light, looking down to find himself in restraints, wrists and ankles. Movement beside him caused him to look up. Beckett was at his side, looking down at him, eyes crinkling in a warm smile.

"Hello," he said, "How are you feeling now, then?"

Sheppard took a moment to consider. "Like death warmed over," he replied bleakly. "What did I do, Doc?" he asked, tugging gently at the restraints.

"What do you remember?"

Again, Sheppard paused, casting his mind back. There were blurred images of whispering voices, the brig, Teyla…

"Teyla shot me with a stunner?" he asked, incredulously.

"Aye, she did. But she only did it to stop you from doing yourself more damage. You were fighting against us trying to get into that cell to help you, son." There was a pause. "Major, something happened to you down on that planet, something that caused you to want to be locked up. You couldn't, or wouldn't tell us then. How about now? Do you feel up to answering some questions?"

John considered. He really didn't want to talk about what had gone on there, but already he could hear the first stirrings in his mind. The whispers were coming back, and so was the pain. Absently he tried to rub at the ache in his temples, only to be stopped by the leather cuff. He tugged it briefly, frustrated.

"I think they can come off if you'd like, Major," Carson was looking at him again.

John was surprised by how certain he was that they should stay. "No." he said, strongly. "No, I think they should stay where they are. I don't feel safe thinking about them coming off." The headache spiked again, and he winced, resisting the urge to try to rub it away.

"Right, they can stay then," said Beckett, "But we can't leave you tied up for ever."

"I know, I know, it's just – I can't remember what they did to make me feel this way. I remember the rest," he closed his eyes, shuddering, remembering, "But why I feel I should be locked up? I just don't know." He pulled at the cuffs again. Harder this time.

Beckett noticed, but said nothing. Instead, he fiddled with writing down the readings from the machinery attached to Sheppard's body. After a pause, he said, "So. I would like to know what happened down there then , so I can treat you appropriately."

"Ask McKay, he was there," replied Sheppard pointing with his head to where he could see McKay sleeping in another bed. Then his voice softened. "He's ok, isn't he? He's not – like this?"

Beckett glanced round at Rodney's sleeping form. "Oh, aye, he's ok. He got a pretty nasty concussion though, because he wouldn't stop pestering the guards about where you were, but he'll be ok. And he can't tell us what happened to you, because you were held separately to them, and they didn't see you after the guards split you up."

Sheppard looked across to McKay again. "He did? A concussion? Wow."

"How about those questions then, Major?"

"Could I have a drink first? And maybe something for this headache?"

Beckett held a glass with a straw in it to John's mouth. The water tasted like nectar.

"No pills for now though," said Beckett, You've got enough chemicals circulating as it is. Tell me what happened," he invited.

Sheppard closed his eyes, and sank back into the pillows. His voice, though deceptively soft had a hard edge to it. "What do you want to know?"

"Why don't you start from the beginning?"

There was a pause, while Sheppard marshalled his thoughts, and resisted rubbing at his head again. The whispers were louder now, insistent, pain throbbed behind his eyes.

"We got through the gate alright," he began, "And it was only a short walk to where they have their community centre. We were ok until we got there…"

His voice trailed off, as he remembered the feeling of hopelessness when they had been surrounded. Men in no nonsense uniforms with projectile weapons had come out of nowhere, or so it seemed and had surrounded them. They were outnumbered, and outgunned. To make a break for it would have been suicide.

One of them came forward from the rest. "Surrender your gun, Major," he said, pleasantly, "Or you will watch while the rest of your team is killed in front of you."

Sheppard hesitated, unwilling to give up even the smallest advantage.

"Quickly, Major, or you can have the pleasure of choosing which one shall go first."

Sheppard shrugged, then handed over his P90, indicating to his team that they follow suit. Ford was more reluctant. "Major," he began.

"Hand it over, Ford, that's an order, "

Reluctantly, Ford complied, as did Teyla, though she looked daggers at the man leading their captors.

"Major, " began Rodney, "I really don't think this is such a good idea,"

"Do you have a better one McKay? Because I'm right out at the moment."

"And the rest of the weapons you have concealed about your person," continued the officer.

Sighing, Sheppard handed over the 9mil and the knife he kept in the small of his back. He watched as Ford and Teyla did the same, even Rodney unbuckling the holster from his thigh.

The officer nodded at his men, and several of them came forward each taking one of the team and proceeding to bind their wrists, Sheppard's behind his back. Then they were frogmarched through the small town's centre until they came to an official looking building where they were escorted inside. They were taken to a large, airy office where an older, more authoritative person sat behind a desk.

"Ah, Major Sheppard, and his team. We were wondering when we'd have the pleasure of seeing you. "

Sheppard was confused. "What's with the third degree?" he asked.

"Forgive us. Your arrival means that a treaty drawn up between ourselves and- another trading partner can finally be ratified. We've been waiting a while for this."

"I thought we were here to trade."

"Indeed you are. We just didn't specify what would be traded. You see, Major Sheppard, you caused our friends a lot of grief, and they would like recompense for their grievances. We have agreed to provide them with the justice they feel they deserve, and at the same time…well, more on that later. Captain Reynar here will see that you are properly accommodated."

Jaq'an turned his attention to the rest of the team, who were looking at him with varying degrees of shock.

"Well. So this is Dr. McKay, Teyla Emmagen, and you must be Ford.

"Now, just wait a minute," began McKay, but was cut off by the same pleasantly lilting voice.

"And you are the one who can build nuclear weapons."

McKay subsided into silence, all of them suddenly realising where the information they had on them was coming from.

Sheppard spoke up again. "You know, apparently, who we are, but we are less well informed. The Genii didn't pass that information along to us."

"Please forgive my lack of manners," replied oily voice. "My name is Councillor Jaq'an, and this is Captain Reynar. Now, you will excuse me if I attend to matters of state. Captain Reynar will have you taken to more appropriate accommodations."

"That's it?" asked Sheppard.

"For now, but we will speak again at a later date, when you are, shall we say, more amenable to assisting us with our plans for the future."

"Don't bet on that," was all Sheppard had to say, before the guards hustled them out and took them down to what could only be described as the dungeon level. There they were separated, and that was almost the last that Sheppard had seen of his team, until Ford and Teyla had arrived to take him home.

Major Sheppard had been taken to a small, cold cell where his hands had been freed. He'd noticed that none of the guards had said a word to him, but that didn't bother him, he had nothing to say to them either. He knew that in a couple of hours, they would be overdue for a check in with Atlantis, and that after that, hopefully, Elizabeth would set in motion plans to get them out. He only had to hold on for a while. The trouble was, he had no idea just how long that while was going to be.

He hadn't been left alone for long before what he knew was coming had started. Two of the guards had come in to the cell, tied his hands and shackled his ankles together with a short length of chain just long enough for him to be able to take shuffling steps. Then a blindfold had been put on, and he'd been roughly marched out of the cell and into another room, which felt much larger, and colder.

He'd been forced to his knees, then without warning, his head was plunged into a tank full of icy water. He felt the ice on the surface break as his head was pushed in. Just as he thought he couldn't hold his breath any longer, his head was yanked out again by the hair, then the process was repeated, again and again.

Once he was 'softened up' he'd been thrown to the floor, gasping and coughing, and then the beating started, fists, feet, rubber hose, whatever. He wasn't able to see what was coming, so was unable to prepare himself to meet what ever was headed his way. It continued until he puked, then he was hauled up again, and taken back to his cell, shivering, where the blindfold had been removed, as well as the shackles round his ankles, but his hands were left tied. There he had stayed for a while, until the guards came back and it all started again.

It had continued in this vein for how long the Major didn't know. His watch had been shattered during the first round, but it felt like hours. Days even. Then, finally he was left alone, in the dark but he couldn't sleep. He hurt too much, he was cold, couldn't stop shivering, and periodically a guard would come round and bang on the door to wake him up.

After what seemed an eternity, the guards came back. No water, no food, not that he would have kept it down, not even any questions. On went the blindfold again, together with the ankle chains and he was forced out of the cell once more. A different direction this time, he noticed as he shuffled along in an ungainly fashion.

This time he was pushed into what felt like a small box, made of metal from the way his boots sounded on it's surface, and for the first time, he felt warm. The shivering stopped, but the heat didn't. The metal quickly became hotter, and hotter until contact with it burned. Trouble was, the box was so small, he couldn't stand straight, couldn't sit, couldn't turn around. Weakened by the treatment he'd received so far, it didn't take long before he was stumbling, trying not to fall onto the hot surfaces. The air itself became hot, until it hurt to breathe. His mouth dried, his nostrils hurt, and he kept his eyes shut behind the blindfold, afraid the heat would sear the delicate surfaces. He hoped and prayed this wasn't happening to the rest of his team. Ford and Teyla might cope, but Rodney? He shook his head, and tried to think about better times. About surfing off the mainland back at Atlantis, anything except his current predicament.

Finally, the guards came back, and he went back to the cell, overheated skin feeling as if it was glowing. The cycle went on. Cold. Beatings. The hot room, sleep deprivation, until his whole world had narrowed down to this cell and what was coming next. Occasionally he was given water, but it made him dizzy, and his stomach hurt, so he drank only when the thirst was overwhelming, then tried to drink as little as possible. At one point, Captain Reynar had paid him a small visit, and spent some time telling him about several of the friends that Sheppard had killed during the Genii raid on Atlantis. After he left, it was a while before the Major was able to stand unaided.

Eventually he was taken back to the same office as he'd stood in before. Councillor Jaq'an was there, still smiling that supercilious smile of his. Sheppard longed to wipe it off. Permanently. He stood, swaying, waiting to see what little gems the Councillor was going to come out with now.

"Major Sheppard," he said, smoothly. "You don't look as well as the last time I saw you."

"Yeah?" grated out Sheppard, "Let me tell you, hospitality in the Pegasus Galaxy sucks. Big time."

"Are you ready to go home yet, Major?"

Sheppard just blinked at him, taken off guard.

"We have already returned the rest of your team. Look"

Sheppard's attention was directed to a small screen at the back of the office. He looked more closely, and saw what appeared to be McKay, Ford and Teyla going through the gate. He looked again at Jaq'an.

"You expect me to believe that?"

"Whether you believe it or not, it is true. We sent them back several hours ago. Are you ready to help us now? Then you can go back too."

"Not helping you, ever," ground out Sheppard. He couldn't believe the rest of his team were home. If they truly were, then Jaq'an was up to something, and if they were, why hadn't Elizabeth negotiated for him. He felt confused, which no doubt was exactly what these bastards wanted. He didn't notice the small nod Jaq'an gave to someone standing just behind him, only became aware of it when he felt a needle plunge into his upper arm, and his knees began to buckle.

He hit the floor, and as consciousness left him he heard Jaq'an say, "You will help us, Major, voluntarily or not." Then there was a loud buzzing noise, and everything rushed away from him spiralling into blackness.

TBC


	4. Chapter 4

PROTECTIVE INSTINCTS part 4

**A/N I'm really touched and excited by all these reviews. Thank you all, very much. And now, on with the story...**

John Sheppard woke up face down on a narrow bench. There was a faint but unmistakable smell of disinfectant. He tried to get up, but was unable to move, due, he discovered, to the fact that he was securely strapped down. He squirmed, testing the strength of the restraints, but they held firm. He could hear voices talking over him, discussing him. They hadn't realised he was awake.

"I refuse to do that," said voice number one, horrified.

"It makes little difference, he is unconscious anyway," said voice two.

"He could wake up at any time, and I will not lower myself to your level of barbarity."

"If he wakens, then we will know much sooner how effective the device will be. It is the Council that has made this request doctor, whether you wish to proceed or not. Please see that it is done."

"And I will, but not without an anaesthetic."

Stunned, Sheppard realised they wanted to perform some sort of surgery on him, and at least one of them wasn't bothered if he was awake or not. He struggled harder, and the two individuals speaking realised he was cognizant.

"He is awake now," said voice one, "and as I said earlier, I refuse to comply with the Council's request on someone who is not sedated. Let me make myself perfectly clear, this is a delicate surgery, and requires the patient to lie completely still if it is to be successful. I cannot guarantee the results if I have to proceed on someone who is fighting all the time. And trust me, he will be fighting."

Sheppard held his breath as there was a pause. There was no way he was going to lay still and let them do – whatever it was they wanted to do. Frantically he tried to loosen the restraints, but only succeeded in taking the skin off his wrists, leaving the cuffs slick with blood.

Voice two spoke up again. "Very well, but this must work doctor, and we have to know soon if it has worked. Anaesthetise him if you wish, but do not fail."

Sheppard felt another needle slide under his skin, and before he could open his mouth to protest, he was asleep again.

The next time he woke, he was back in the original cell. Groggily he sat up, head spinning, wondering what had happened this time. Abruptly he remembered, and sitting up straighter, felt all over himself for any incision marks, but could find none. He felt…different, though he couldn't put a finger on what it was.

The door to his cell opened, and he looked up dizzily. Councillor Jaq'an stood there, flanked by two of the guards that Sheppard had gotten to know unfortunately well. Jaq'an looked down at Sheppard contemptuously, but said in the same oily voice, "Ready to go home now, Major?"

"Wha'?" began Sheppard stupidly, still under the influence of whatever drugs they'd given him.

"Dr. Weir has been successful in negotiating for your release. Come."

Sheppard tried to stand, but was unable to get up. There was a faint hissing noise in his head. The guards picked him up, and tied his hands again. His wrists hurt, but it felt distant. He didn't really notice. 'Helped' along by the guards, he was taken back to the Stargate where he saw Teyla and Ford along with a couple of marines waiting to take him home, but something didn't feel right. He didn't want to go; there was something wrong with him, something that was making him feel that taking him back might be dangerous to Atlantis.

He turned to Jaq'an, not quite believing. "Is this real?" he slurred.

"It is, Major," replied Jacq'an smoothly, pushing him forward towards his team then stepping back. Sheppard would have fallen if it weren't for the quick actions of Ford and Teyla who stepped up smartly and caught him before he hit the ground. Without another word, the Suventan delegation turned and walked away.

"Good riddance," muttered Ford, turning his attention to his commanding officer. "Are you alright sir?" he asked, noticing that the Major didn't seem quite with it. He started to undo the bindings around Sheppard's wrists, but stopped when the Major grabbed his hand.

"Leave them on," whispered John peremptorily.

"But Sir –" began Ford.

"That's an order, lieutenant."

"Yes sir," replied Ford. "Let's get you home, Major. Dial it up," he ordered one of the waiting marines, and after the wormhole established itself, assisted him home.

Sheppard finished his account, and lay back, exhausted. The headache had become an eight on a scale of one to ten, and the whispers were louder, buzzing in his head, trying to get him to do something. He fidgeted, pulling at the restraints again, wanting to hold his head, try to block out the susurration of distant voices.

Beckett had said very little during the tale that Sheppard had told him, but the anger was back, and he was struggling to control it. He glanced at the Major, and noticed the line furrowing his forehead, and the way he was fidgeting, pulling gently at the cuffs holding him down.

"Headache bad?" he asked sympathetically.

Sheppard nodded briefly, trying to move his head as little as possible. "The whispers are worse. Is there anything you can give me to stop it?"

"Whispers?" Beckett asked. This was the first he heard of those.

"Yeah, whispers in my head, like far away voices. There's something they want me to do, and I don't want to do it. But the more I resist, the worse they get, and the headache gets worse too. You've got to give me something, Doc."

Sheppard didn't want to sound like he was whining, or worse, begging, but something was going to have to give soon, and he didn't want it to be him. "Please?" he whispered begging anyway. "I don't know how much longer I can hold out."

He was aware that Beckett was fiddling with the IV port in his hand, and risked opening his eyes to take a look. A warm fuzziness spread through his veins, and his voice sounded slurred and distant when he said, **"**Better. Tha's better. 'nks…doc…" and he began to slide away, grasping suddenly at Beckett just before he went completely under. "Don' take…off the…cuffs…" and he was gone.

Beckett stood a while longer looking at Sheppard sleeping. His face had evened out, and for the first time since they had got him back, he looked peaceful. Which was more than Beckett himself felt. He knew that Sheppard had given him the bare bones of what had happened down there, that he'd left out a lot, such as a man's fingernails didn't look like that just because he'd cut them a bit shorter than normal. He'd seen the bruises, some of them boot shaped, that covered the Major's body, and the burns… he could go on, but instead decided to do a more thorough examination, looking for signs of recent surgery. He called one of the nurses to help him turn the sleeping figure over.

TBC


	5. Chapter 5

PROTECTIVE INSTINCTS part 5

**A/N the bunnies thank you all for feeding them so well. A slightly shorter chapter this time, and I'm afraid its all going downhill for the Major from here.**

McKay came awake with a snort, and saw Beckett sitting in the chair by his bed, looking at him, eyes crinkled with humour.

"I was not snoring." He said crossly.

Beckett chuckled. "No," he replied, "Calling it snoring wouldn't be doing it justice." His eyes lost their humour, and he glanced across to the screened area where the Major was sleeping for the moment. Rodney followed his gaze.

"Carson?"

Beckett regarded him again. "How're you feeling now then, Rodney?"

"Apart from the brass band currently playing in my head, absolutely fine. How is he?" he gestured to the Major's bed.

"He's not good, Rodney. In fact, if you're up to it, I could use your help."

"Of course." McKay struggled to a sitting position, ignoring the slight dizziness. "What can I do?"

"I think the people on that planet may have implanted some kind of controlling device in the Major, but I can't find it on simple examination. I'll be doing an MRI scan shortly, but I was wondering how they're using it. Maybe there's a signal being transmitted from them to the device. If there is, maybe we could block it. It might at least give him some peace."

"Peace? How so."

"Major Sheppard is complaining of hearing voices." He paused at Rodney's look of dismay. "No, not those sort of voices. He says they are whispers that he can't really hear clearly, and that they're trying to get him to do something he doesn't want to do. He says when he resists, it causes pain. I suppose there is a similarity to schizophrenia, and I'm worried about what will happen to his mental state if we can't stop it."

Rodney swallowed. "You mean it could drive him mad?"

"Well, I don't really know. If he continues to resist, I think eventually he'll burn out. If he gives in, and does what they want, then he'll have to live with that for the rest of his life. And I don't think he'd do that for long."

Their eyes met.

Rodney got out of bed, holding onto it for a moment when the world briefly tilted. He looked at Carson again, hoping the doctor hadn't noticed. He didn't want to be sent back to bed. If Carson wanted his help for the Major, then Rodney wasn't going to let a little dizziness get in his way. He squared his shoulders, and put on the Rodney persona that everybody knew and loved.

"I'm not doing this in scrubs," he stated, holding out his hand with a double snap of his fingers. Carson handed him the clothes he'd been holding.

"Take your time Rodney. I won't be doing much until the sedative wears off." He walked away to check on the Major again.

oOo

Sheppard lay on the narrow confines of the stretcher that was part of the scanner. He'd woken from the drug-induced sleep, but was still a bit groggy. Already he could hear the whispers, the sound rising and falling, and he felt anxious. He didn't want to do this, but he wanted all of it to end. Beckett had removed the restraints, telling him they were out of place in a scanner, and Sheppard knew that Ford and Teyla along with several other soldiers were guarding him, but he still felt vulnerable. No, that was the wrong word. He felt like a time bomb waiting to go off.

From his position on the scanner, he could just see Carson bustling about, and Rodney standing to one side, looking anxious. He sighed, and it hurt his ribs. He didn't want to be putting his friends through so much anxiety on his behalf, but he acknowledged he needed their help. He wasn't going to be able to do this alone. McKay had told him they had checked him for signals being transmitted, but hadn't found anything. His own anxiety notched up a level. What the hell had been done to him, and why? The thoughts skittered around in his mind. 'They' wanted Atlantis, or they wanted it destroyed. He wouldn't do that, couldn't do that. Could he? The headache started again, blinding flashes of white light searing across his skull. It was so hard to think when it hurt like this.

He was aware that Beckett was talking to him, heard the machine powering up, and then Sheppard's world exploded in an eruption of white hot pain, raw agony exploding across all his nerve endings. He did the only thing he was capable of doing at the time. He screamed, and screamed…

oOo

McKay stood quietly and watched Beckett getting the Major ready for the scan. They'd helped him onto the narrow bed angling into the machine itself, and Beckett had been adamant in his refusal to tie Sheppard down again, arguing that the Major could resist for the few minutes it would take to perform the scan, and that anyway, Ford, Teyla and several other guards were there to stop him from doing anything. Sheppard, still not fully awake had just nodded, and sighed, lying down trying to find a comfortable spot where his aching body could rest.

Rodney had been horrified when he'd seen what had been done to the Major, and didn't know how the man could still be functioning. He felt guilty that his own efforts to help had come up with nothing. If the Suventans were using some kind of signal to control the device, then he, Rodney McKay couldn't find it. Yet. He watched as Beckett fussed with the machine, telling Sheppard to lie still, and powering the thing up. But he wasn't prepared when suddenly Sheppard's body arched off the stretcher and he began screaming like all the demon's of hell were after him…

oOo

Beckett saw the Major properly positioned on the scanner bed, then went behind the screen to check the final settings. The monitors recording Sheppard's vital signs were showing that the Major's pulse rate and blood pressure were up slightly, but in view of the amount of adrenalin already circulating, Beckett wasn't surprised. Still, John was going to have to keep still if this was going to work. He bent down to the microphone connecting him to the man in the scanner, and spoke reassuringly.

"Major, we're about to start. You need to keep still now, that's really important." He watched as the man stilled, checked again that the people he'd asked to come and guard the Major were all in place. This was the only way he'd managed to persuade Sheppard to have the scan done without restraining him, and he was not tying anyone down during an MRI scan. Checking the Major's vitals again, he noted the pulse rate was even faster. Time to get on with it. He turned the machine on, head snapping up in alarm as Sheppard began screaming.

Quickly he powered the scanner down, then ran to the stretcher where Sheppard was still thrashing and yelling. Gesturing for Ford to help, he slid the stretcher out, hoping that would be enough to calm the man, but to no avail.

"God, Doc! Make it stop!" Sheppard was grasping at his arms so tightly Beckett wouldn't be surprised if there'd be finger shaped bruises later, twisting and turning as if he was trying to escape some kind of torment.

"Major! John, you're alright. It's stopped. Calm down lad, we're here to help you." Beckett's words were having no effect. He nodded to Ford to take over holding the Major. Ford complied, eyes wide with alarm, but doing his best to talk his CO down. Beckett ran to the medical supplies and returned with a loaded syringe, but John, catching sight of it decided enough was enough. No more drugs, no more controlling him.

Drawing back his arm, he drove a powerhouse punch straight at Ford, knocking the lieutenant flying, grabbing the stunned man's gun in the process and leapt up, grabbing at Beckett as he did so. He wrapped an arm around the Doctor's throat, then used the other hand to smash the hand that was holding the hypodermic into the side of the scanner, once, twice. With an indrawn hiss of pain, Beckett let go the syringe, and it dropped to the floor, needle embedding itself harmlessly in the ground. Now Sheppard was using the Doctor as a human shield. Slowly retreating, dragging the struggling medic as he went, waving Ford's 9 mm around threateningly. None of the soldiers could get a clear shot at the Major, and anyway, they didn't want to injure their CO any more than he was. Sheppard exited the room, and fired the gun into the door locking mechanism as he went, ensuring no-one could follow him in the near future. Beckett was still struggling, so without compunction, Sheppard smashed the butt of the handgun against the side of the Doctor's head, then scooped up the unconscious man, ignoring his own screaming ribs, and started off at a shambling run down the corridor, trying to get as far away as he could go.

TBC


	6. Chapter 6

PROTECTIVE INSTINCTS part 6

**A/N once again, thank you all so much for the reviews you've sent. I'm turnong into a real fb junkie!**

Beckett woke up with a groan. His head hurt, his stomach roiled in the most unpleasant way, and he didn't know where he was, except that it was cold and hard. He risked opening his eyes, and saw Sheppard sitting on the opposite side of the room from him, back against the wall, knees drawn up to his chest, elbows resting on his knees. His head was resting on his arms, and the gun dangled loosely from the Major's grip, but Carson had no illusions that he wouldn't use it.

The doctor realised he was lying on the floor, and it was most uncomfortable. Carefully, giving every consideration to his aching head, he pushed himself up, slowly. The world tilted, spun lazily, then settled , which was more than Carson could say for his stomach. He propped himself up against the wall, mirroring Sheppard, then gave a short hiss of pain as he tried to lean on his injured hand.

Sheppard's head came up quickly as he realised the doctor was back in the land of the living. "You ok, Doc?" he asked.

Beckett felt the side of his head that was sore, and encountered sticky, almost dried blood. So. He hadn't been out for too long then. He started to nod, thought better of it, then answered, "I'd be a lot better if someone hadn't used my head as a battering ram."

The man across from him had the grace to look abashed. "Sorry about that Doc. I just- I just had to get away. I knew they wouldn't let me go, so I brought you along as hostage. Sorry," he offered again.

Beckett contented himself with a short grunt of acknowledgement, then leaned back and closed his eyes again. Gradually the dizziness was improving, though he was sure he had a mild concussion. Again. He felt cloth around his sore hand, and looked down. Crimson fabric, the sort the scrubs were made from was wrapped around the bruised knuckles, and Beckett regarded it curiously, realising that Sheppard must have bandaged it while he was out of his senses.

He looked over to Sheppard again, and saw that the man had returned to his previous position. "How are you doing, lad?" he asked gently.

"Oh, I'm just fine." He replied. Carson could see that Sheppard was trembling, from cold or something else, he wasn't sure.

"We should get you back to the infirmary," he said, then recoiled slightly, as the Major's head shot up, and he looked at him with fever bright eyes.

"No, no, not going back. Not going back there, no." He started to rock slightly, back and forth. "Can't make me, not going back. Sorry, doc, sorry, shouldn't have brought you into this. Not your fault, but not going back there, ever." The rocking picked up apace.

Carson looked on, feeling helpless. "I can't help you here, laddie, but maybe I can find a way to stop this back at the infirmary."

John looked at him again, the rocking momentarily stilled. "They're winning, Carson," he said softly. "They're winning. I can't keep this up anymore. It's only a matter of time. They'll find me, and when they do, it'll be restraints and drugs, and it won't help. It won't help, because whatever they did, its still there, and it won't go away until I've done what they want. And I can't do it. I won't do it, but I'll have to, because in the end I'll give in. I won't be able to stop it for ever, and then all this will be gone, and it will be my fault, and you'll all have gone too and you'll all hate me and- I can't do this anymore, I can't do this…"

His voice trailed away into silence, and the rocking started again. Beckett stared, not sure what to say. He watched as Sheppard became increasingly agitated, finally getting up and beginning to pace.

John Sheppard knew he was losing it. Dragging Beckett here had proved that. The voices were incessant, never letting up, never letting him think clearly for himself. He was finding it harder and harder to stay oriented to where he was, on Atlantis, or Suventa. His bare feet slapped the ground as he got up and began to pace, hoping the movement would help to clear his head, just a little, just enough to let him think.

"Major, I'm sure there's more we can do, if only you'd let me try."

The pacing stopped, and in a flash, Sheppard was invading Beckett's personal space, fists twisted in the front of the doctor's white coat, eyes blazing. He shook the unfortunate medic like a terrier with a rat.

"Why can't you understand! I'm NOT going back to be poked and prodded and experimented on. You don't know… you don't understand…"

He let go abruptly, the anger dissipating as fast as it had come, leaving him exhausted, hurting, shaking, scared. He avoided eye contact with Beckett, who was rubbing at his sore chest where Sheppard had held on so tightly. As suddenly as it had started, the attack was over, and Sheppard retreated again, shambling, pacing unsteadily, muttering.

"Sorry, sorry, didn't mean to…sorry, not your fault…wanted to…"

Beckett couldn't catch the rest, but he began to feel truly afraid, not for himself, though he was apprehensive about what the Major might do next, but for the man in front of him, who was surely losing it. He sat back against the wall, feeling the solidity, a reassuring bulk, and wondered what would happen next. He knew they'd be found soon, the lifesigns detector in the control room would show them up soon enough, but he seriously wondered what it was he was going to do when they eventually got the major back to the infirmary.

After a few moments, booted feet could be heard getting closer. Sheppard looked up again, face frantic. He turned to stare at Beckett, and the doctor was struck by the expression of bleak helplessness that was in the Major's eyes.

"Help me, Carson, please. Please don't let them-"

Whatever else Sheppard was going to say was lost as the soldiers skidded around the corner, training weapons on both men. Bates was in the front, pointing a P90 directly at the Major.

"Doctor Beckett," he said, looking briefly in the doctor's direction. "Are you alright?"

"I'm ok," replied Carson, "But we need to get Major Sheppard back to the infirmary."

Sheppard scrambled to his feet, bringing up the gun again. "I am not going back." He said, though Beckett wasn't sure if he meant the infirmary, or the planet. One of the medics approached Beckett, carrying a medical kit, and Carson waved him away, then had a second thought, and asked for the kit to be brought back. He rummaged around inside, finally finding what it was he was looking for. Nodding to the medic, they prepared a syringe of sedative between them. It was done so quickly that Sheppard hadn't realised, until he heard Beckett say, "Right then, Major, you're safe here now son. Let us help."

Carson gestured to Bates to manoeuvre his men to take Sheppard. John's eyes narrowed.

"Don't," was all he said.

"Major, you know we only want to help you."

"No, I don't," replied Sheppard. "I can help myself, stop all of this right now. No more, no more voices or pain or…" he raised the gun to his own temple.

"NO!" shouted Beckett, distracting the Major just long enough that Bates was able to take him down in a flying tackle. More soldiers piled on top, restraining the Major, who fought back for all he was worth.

Beckett hated to do this, but John needed more help than he really knew. He approached him with the syringe, again. Sheppard's eyes opened wide, pupils dilated with fear. In his confused state, he wasn't sure if he was on Atlantis, or the planet, but one thing he was sure about, they weren't going to do this to him again. He saw Beckett looming over him with the needle poised, and something within him snapped. Suddenly he went absolutely still, just as Carson was about to plunge in the needle.

Beckett stopped suddenly, and Bates shouted for him to get on with it.

"No," said Carson, voice suddenly flat and emotionless. "You can let him go now"

"What?" began Bates, but got up anyway. Beckett knelt down next to John, favouring his injured hand, and looked sadly into the wide open eyes of his friend.

"It's alright," he said heavily, "The Major won't give us anymore trouble just now."

"Is he dead?" asked Bates fearfully.

"No, he's…just not there anymore."

And it was true. John Sheppard had simply gone away. And, on Suventa, Councillor Jaq'an allowed himself a small smile as the receptor of the device finally beeped a warning that the subject had achieved the desired state of receptiveness.

TBC


	7. Chapter 7

PROTECTIVE INSTINCTS part 7

**A/N Sorry about the short delay in posting this part. RL has caught up with me I'm afraid.**

Carson Beckett scrubbed at his tired eyes, then reached into the drawer of his desk for the Tylenol. It had been a long few days, and the guilt hadn't abated any. He looked up again, checking on the Major without really knowing he was doing it, sighing when it was apparent nothing had changed. Not that he was expecting anything to have changed, but he could hope. He swallowed the medication with a sip of lukewarm water that had gone stale from sitting on his desk for too long, mentally reviewing the past few days, trying to find anything that he could use to help the man currently in the bed on the other side of the infirmary, or anything to assuage the guilt that was preventing him from sleeping.

The first few hours after Sheppard had dragged him along as hostage were unclear; he had after all had a concussion himself, and even now the headache lingered slightly. He had woken in a bed next to Sheppard's and that had been fine to start with, he could check on the Major's condition without leaving the comfort zone of his own bed, but after 36 hours, he'd been discharged back to his own quarters. He'd spent a fruitless day there scouring the medical texts he'd brought with him trying to find any information on catatonia, and methods of rousing patients from such a state, but there was very little, trauma surgeons rarely having to deal with such occurrences.

After a day spent doing an information search, then a night spent waking sweating from dreams in which Sheppard variously shot him, became unresponsive, or died, he'd had enough, and reported for work the next morning, ignoring the advice from his own doctor that he should still be on downtime. He'd snapped at the nursing staff, barked orders at his medical team, and had been so thorough in giving post mission check-ups that eventually he'd been left alone, a situation that suited him well given his current feelings. Even Elizabeth, who at the request of the infirmary staff had come to try to talk him out of it had eventually left, reasoning that behaviour so unlike their CMO would eventually work out of his system.

And it had, and after apologies all round, they had settled back into an uneasy routine, the silent presence of the Major preventing the easy camaraderie they had become used to. The nursing staff were doing everything for John, he was incapable of doing anything for himself, and it was only their dedication that was preventing his physical condition from deteriorating. And that was puzzling Beckett. After several days of complete inactivity, he would have expected at least the beginnings of muscle atrophy, and other signs that Sheppard's body was not being used, and yet there were none. It was as if the man were simply sleeping, but the wide open eyes, the vacant expression and lack of response gave lie to that.

The infirmary was quiet, it was night and the lights were dimmed. The peaceful background combined with the steady and monotonous beep, beep, beep that came from the cardiac monitor attached to Sheppard, the only piece of equipment currently in use, began to have a soothing effect on Carson, gradually lulling him off to sleep. He was, frankly, exhausted, both physically and mentally. His inability to get a decent night's sleep combined with the thoughts that kept running round his head, the _'I should have_ _seen it coming; I should have found a way to prevent this'_ thoughts were draining him. Gradually his head began to lower, his eyelids drooped, and within a short space of time, he was asleep, head coming to rest gently on his desk.

He awoke sometime later with a crick in his neck, and a feeling something wasn't right. Disorientation struck him first, and it took a few minutes to work out where he was and why he was where he was. It was always like that when he was exhausted from being on call, but gradually recognition filtered through.

"Bloody Hell," he thought, lifting his head quickly from the desk, and wincing at the stiffness in his neck. Just how long had he been out? Judging by the congealed skin on the top of his coffee, it had to have been a couple of hours, at least. The feeling of 'wrongness' persisted, and looking round the infirmary, he felt it was too quiet. His heart skipped a beat when he realised the Major was gone, and had been for quite a time. When he checked, the bedding was cold, and the blood left from where the IV had been torn out was long dried into the linen.

At first, he stood there, conflicting emotions preventing him from deciding what to do. On the one hand he was delighted that Sheppard appeared to have come out of the catatonia, on the other hand he was filled with dread as to why that should be, and what he was up to now. The infirmary was empty, of that he was sure. There had only been himself and Sheppard there, he'd sent the duty night nurse off a while ago. Standing a moment longer, indecision rooting him to the spot, he finally decided he had to go and find out just exactly what was going on. He was momentarily surprised that the infirmary was locked, but shrugged it off and used his medical override to open the door.

First port of call, John's quarters. That's where he usually went when discharged from the infirmary, and it seemed as good a place to start as any. No need to inform Elizabeth or the duty security team if all the Major was doing was sleeping in his own bed. Moving along the corridors though, Beckett began to feel something was definitely wrong city wide. The lighting was dimmed as was usual for night time, but even so the doctor would have expected to see an occasional security guard, or scientist pulling an all nighter wandering the corridors. There was no-one, and his apprehension kicked up a notch. For some reason, the thought of calling the control room made him feel uneasy, so he held off for now. Just until he was sure.

By the time he had got to Sheppard's door, he was sure, but went through the motions anyway, again using his medical override to disengage the lock. No-one there, and by the looks of things, there hadn't been anyone there for a long time. By now feeling very anxious, and still with that curious reluctance to call the control room he decided to head there himself, and find out what was going on.

On the way, he tried calling Elizabeth and Rodney on their communicators, but got no reply, and that was unusual in itself. One of them should have responded. Carson Beckett was a doctor. A medical doctor, not a commando, but he could rise to the occasion if he needed to, and this seemed to be one of those occasions. He felt a detour to the armoury was needed too, and headed off in that direction.

Once there, again he had to use his personal authorisation to override the locking mechanism, and stepping inside tried to choose a suitable weapon for whatever might lie ahead. After spending a short time variously selecting then discarding several pieces, he ended up choosing a Wraith stunner, deciding that if he made any mistakes, at least the person he'd shoot would eventually get up and walk away. He quietly exited the armoury, re-locked the door, turned and walked straight into Major Sheppard.

Startled, he stepped back. Sheppard looked at him, face expressionless in the dim light.

"Major," began Carson, "I wasn't expecting to see you here. How're you feeling now then?"

Sheppard said nothing, and Beckett began to feel uneasy. He backed up a little, noticing that the Major followed.

"Major Sheppard, stop right there!" barked Beckett with an authority he didn't feel, hoping it would cause John to stop. When the Major carried right on coming, he tried for a different tack. "You should come with me back to the infirmary right now," he said gently but firmly, still backing up. The Major remained expressionless, and most disturbing of all, silent

Suddenly Beckett found himself being pushed back up against the wall, and none too gently either. "Put me down," he wheezed, gasping as Sheppard's hands squeezed around his neck, lifting him off his feet, back still forced up against the solid surface.

Sheppard did as bid, tossing the medic to the floor as if he weighed nothing. Beckett lay for a moment gasping, then realised the Major was coming in for another turn. He scrambled back, hand accidentally brushing against the stunner that he had dropped in the initial skirmish. Sheppard noticed, and kicked the weapon out of Beckett's reach. Beckett lunged after it, seeing stars as the Major's foot connected with his lower back. The Major followed him as he tried to crawl away, picking him up, and pummelling a fist into Beckett's midsection. Carson folded over, desperately trying to draw breath into his bruised lungs, when Sheppard's fist again made contact, this time with the medic's jaw. Beckett sprawled on the floor, seeing stars again, but realised he'd landed on top of the stunner.

With a turn of speed he didn't know he possessed, Carson snatched up the weapon, pointed it at Sheppard, then fired, not knowing whether to feel remorse or relief when the Major dropped at his feet. Something fell out of John's pocket, and lay glinting in the reduced lighting. A set of small keys. Carson scooped them up, not knowing what they were for, but reasoning they were probably important, and stuffed them into his own pocket. Then regretfully looking down at Sheppard, beat a hasty retreat towards the gateroom, limping against the soreness where John's bare foot had connected. The worst thing about the whole attack was that Sheppard hadn't uttered a sound, not one, and all the time his eyes had held that peculiar emptiness, as if he wasn't really there at all. Beckett couldn't have been more wrong. Sheppard was aware of every thing his body did, but was powerless to prevent it, and the anger inside was building.

By the time Carson made it to the command centre, he was feeling totally unnerved. Atlantis was like a ghost town. There was nobody in the place other than himself, it felt like, and when he finally reached his destination, he understood why. He found a vantage spot in the shadows where he could see what was going on without being seen himself unless someone was looking hard, and from where he was, he could see Elizabeth, Rodney, Ford, Teyla, Bates and Zelenka, chained together and then secured to the railing running around the balcony. He couldn't see anyone else, but felt sure they were all securely held somewhere also. After all, Sheppard would only have needed to access the main computer and use his gene to lock every door in Atlantis if he'd wanted to. The only doors he himself had needed to access had been locked, he mused, but then he'd expected them to be. And why he himself wasn't being held at gunpoint with the rest? Well the jury was out on that one, maybe Sheppard hadn't noticed him in the darkened infirmary, and, he had to admit, the Major didn't act as if he was firing on all cylinders right now anyway.

The command team were locked together with handcuffs, and for once, Rodney was quiet, looking more shell-shocked than anything. Movement close to the group of Atlantis personnel caught his attention, and he was astounded to see Sheppard there, checking his prisoners were still securely held. It was impossible. The man shouldn't have been able to recover from a stunner blast that quickly! He watched, stupefied as the Major then went over to the main computer, and dialled out.

The wormhole established, and in a flat, expressionless voice, Sheppard told whoever was on the other side that Atlantis was secure. The worm hole snapped shut, then almost immediately, the gate began dialling again, this time an incoming wormhole. Beckett craned to see the address lit up on the DHD, but was unable to from his vantage point, not that it would have meant anything to him anyway, but he felt any information would be useful at this point.

Elizabeth's shocked "What do you think you're doing?" dragged his attention away from the DHD and the expression on her face chilled him. He wasn't given long to ponder though; people were coming through the gate, and to his horror, he saw it was Commander Kolya, and Cowan from the Genii.

oOo

The two senior Genii commanders strode into Atlantis as if they owned it, and judging by the small size of the military contingency they had brought with them, they must have thought it was theirs too. '_Well,'_ thought Beckett, '_not if I can help it.'_ He watched a moment longer, as Kolya walked around Sheppard, looking at him like he would look at an interesting specimen in a museum. He leaned into Sheppard's personal space, grinning like the cat with the cream. Sheppard merely stared ahead, totally oblivious. Around them, the Genii soldiers were moving into strategic positions, one of them standing guard over the captive Atlantis personnel. Carson sighed again. He hated violence, and it seemed as if there was going to be no other way to get out of this one. He began creeping quietly to the rear of the handcuffed group, hoping no-one would notice and give him away.

He heard Elizabeth take in a sharp breath, and Rodney cried out, "What do you think you're doing?" He risked a quick peek, and saw the Major on the ground blood dribbling from a split lip, Kolya standing over him. He winced as Kolya let fly with a couple of kicks that were bound to cause more damage, but Sheppard remained passive throughout, not flinching, not moving. Carson chose to move a little more quickly, ignoring his aching body, taking advantage of the distraction caused by Kolya's actions. He heard rather than saw Kolya lash out again, then give up in disgust.

"There is no challenge in this!" he spat. "No honour in taking on a man who is unable to defend himself. But there are other ways a man can get his revenge." He heard Kolya move away and begin conversing with Cowan, both in low voices. And that was when things began to go wrong for Carson. Suddenly Sheppard was there, staring down at him, and he found himself hauled up unceremoniously, disarmed, and marched to where Kolya stood.

"Well, done Sheppard," said Kolya, ironically. Who do we have here?"

"Ma name is Carson Beckett. Ah'm the Chief Medical Officer here," replied Carson, accent thickening as it always did when he was under stress.

"Do we need him?" questioned Cowan.

"I think not," replied Kolya

"Then kill him."

"No, wait!" called out Elizabeth. "Dr. Beckett could be useful to you, he also has the ancient gene."

"We have our own healers, Dr. Weir," replied Cowan. "And Major Sheppard will give us as much access to the Atlantean technology as we could possibly want. He won't be able to help himself. Dr. Beckett is just one more useless appendage to our takeover. Kill him."

An evil gleam appeared in Kolya's eyes. He took the P90 that Sheppard had been holding until the arrival of the Genii and gave it back to him. "Stand up!" he ordered the quiescent Major. Sheppard obeyed, standing before Kolya like a Zombie, gun loosely held. Kolya indicated Beckett. "Kill him," he ordered the Major.

"Wait!" said Cowan. "Kolya, you know the Suventans said that too much stress was the only thing likely to cause us to lose control over Sheppard. Don't push him too far."

Kolya merely said, "Carry on, Major."

There was the briefest of hesitations, then Sheppard turned to face Beckett, and drew the gun up to his shoulder, regarding the medic with expressionless eyes.

Time slowed for Beckett; all he could focus on was the barrel of the gun pointing at his chest. Dimly he was aware of Elizabeth, Rodney and Zelenka pleading with their captors to stop this insanity, but it was the look in the major's eyes that finally caught his attention. Bracing himself, willing himself not to close his eyes, he stood straighter while Sheppard flicked off the safety….

TBC

It always helps the bunnies to have lots of feedback. Yep, its their favourite food...


	8. Chapter 8

PTOTECTIVE INSTINCTS part 8

**A/N So sorry for the delay in posting this chapter, blame RL. The next part may be a while too...**

Carson stood, facing the gun, drawn up to his full height. He looked squarely at Sheppard, and said in a low voice, "This isn'ae your fault lad, so if you ever wake up, don't beat yersel' up over it." Something flickered in Sheppard's eyes, and Carson felt a sudden irrational fleeting hope. It died as the Major settled the weapon more comfortably into his shoulder. Sighing, Carson closed his eyes, making peace with himself.

The sudden report as the gun fired took him by surprise, and he jumped, startled, but was even more surprised to find himself still on his feet, and apparently still in one piece. He opened his eyes, jaw dropping as he took in the scene before him.

On the floor in front of him lay Cowen, definitely dead, but still twitching, blood pooling beneath the body. Feeling as if he was in a dream, he looked up to find Sheppard had Kolya securely held, the P90 pointing at his head.

"Carson? You OK?" Sheppard flicked him a glance.

Beckett nodded, speechless, still feeling in the dream state.

"Good. Go up there," he pointed with his gun, "And get every one free."

To the Genii in general he said, "Drop your weapons, and kick them over here. I will shoot anyone who tries anything."

The soldiers looked to Kolya, who after the briefest hesitation, accompanied by Sheppard grinding the gun further into his temple, briefly nodded his assent. The sound of metal hitting the floor had never been more welcoming. Carson hurried to the upper balcony, retrieved the keys and hastily set about freeing Elizabeth, Rodney and the rest. Rodney sat down hard once his were off, breathing furiously.

"I, thought-" he said, "I thought he was really going to shoot you."

"Aye," replied Beckett, "I thought he was too." And sat down beside his friend, legs suddenly unable to support him, arms wrapped round his aching ribs.

Once The Atlanteans were free, they set about disarming the remaining Genii and herding them together in front of the Gate. Sheppard still held a weapon on Kolya, but could feel himself weakening, and knew this had to be over soon. Unfortunately, Kolya could feel the Major's diminishing strength too, and was merely biding his time, waiting for the right opportunity.

Sheppard had woken in the infirmary, and had been aware of his body moving under control other then his. He was unable to exert any influence over it at all, and had watched, detached as his hands had removed the various pieces of medical equipment, IV, catheter etc, and had silenced the cardiac monitor before its alarm could wake the sleeping medic. Still as a passenger in his own body, he had only been able to sit by, figuratively, and watch as one by one he'd woken Elizabeth, Rodney, Zelenka, etc, and had taken each to the control room, handcuffing them and making it impossible for them to get free or warn the rest of Atlantis what was going on. Knowing that whoever was controlling him was using his own knowledge against his friends and colleagues had at first made Sheppard resentful, then downright angry. Being …forced somehow to go after Beckett, then beat on him, even as he was resisting with every fibre of his being had all added fuel to the fire growing within him.

It was as the anger grew that he sensed the controlling forces weakening, and had determinedly carried on fuelling that anger. It hadn't been hard. All he'd had to do was think back over the previous few days, the torture, the humiliations and degradations they'd performed on him. Add to that the forced surgery, Carson, and now this…the anger had blown up to huge proportions. It still wasn't enough. He was still unable to break the control, and had watched, horrified as he allowed the Genii to just walk in and take over. He was unable to stop Kolya gloating over him, had been unable to prevent the beating the man had given him in front of the whole command crew.

But it was when he'd been ordered to shoot Carson that something within him had finally managed to overcome the control. It was the last straw, and he wondered how Kolya would feel when he told him as he was most assuredly going to that he himself had been the instrument of his own undoing. Seeing the normally affable medic standing before him, seemingly unafraid when Sheppard knew the man had to be quaking in his boots; that had been when he felt the shackles slip, but the supreme moment came when he heard Beckett forgiving him for something he was unable to prevent. Suddenly he was master of his own destiny again, and he wasted no time in putting it to good use. He somehow had to make up for all he had done, and right now, that meant getting Atlantis back into their own hands.

It had felt very satisfying to shoot Cowan, but he wanted to savour Kolya's death. He wanted the man to feel the despair that yet again his mission to take over Atlantis had failed would bring. Unfortunately the adrenalin surge that had enabled him to shake off the control, was also wearing off, and he was beginning to feel each and every injury, feel them beginning to slow him down.

Beckett saw it too. "Ah, crap," he said, and stood, wobbling, in preparation to go down and help the Major.

"What? What?" asked Rodney in that rapid fire way of his.

"The Major's just about dead on his feet," replied Beckett hurriedly. "He's not going to be able to hold out much longer, and he needs help." He scurried down the stairs towards Sheppard, calling out for Ford and Bates as he did so. Ford quickly took in what was happening, and, scooping up some of the Genii's discarded weaponry headed after Carson, tossing a gun in Bates' direction as he did so. Rodney and Elizabeth, waiting only to gather some of their own weapons, weapons they were more familiar with, hurried after them, Elizabeth taking a few more moments to disengage the locks on all the doors, and putting out a city-wide call for armed security to the Gateroom.

Kolya sensed his moment, and stumbled, catching Sheppard off guard. The Genii commander twisted, and grasped at Sheppard then removed the P90 from him as easily as taking candy from a baby . He shoved the Major at Beckett's rapidly advancing form, causing John to virtually fall into Beckett's oncoming body. They stumbled, locked together, but miraculously didn't fall. Then Sheppard saw Kolya raise his gun, pointing it at the two men.

"Goodbye, Major," gloated Kolya, pulling the trigger.

Sheppard tried desperately to twist and push the Doctor out of harms way, but the shot came too quickly, and they hit the floor in a tangle of arms and legs, and a welter of blood. They lay ominously still…

TBC

Thanks for all the feedback, folks, it really makes my day.


	9. Chapter 9

PROTECTIVE INSTINCTS part 9

**A/N so sorry for the long delay oin posting this. To make up for it, I'm posting parts 9 and 10 together, and then it's complete! Thanks for your patience, I hope its worth the wait.**

Elizabeth Weir stood for a moment in the control room pausing to regain her composure. The last few minutes, hell, the last few hours had been difficult, but it had been the last few minutes that had really shaken her.

The Genii had been quickly disarmed, and were on their way to being sent home when a warning shout had snapped her attention to where Sheppard was holding Kolya. To her horror she had watched helplessly while Kolya had somehow gained the upper hand, and had sent the Major stumbling into Beckett. The next few moments played out as if in slow motion. She had seen Kolya raise the gun, had watched as Sheppard had desperately tried to push Carson out of the way, and had seen them both go down as the Genii commander's bullet found its mark

Ford had already been on his way, and had wasted no time in putting a bullet of his own into Kolya. The Genii fell to lie beside Sheppard and Beckett, and all three lay still, unmoving, blood pooling beneath them.

After that, there had been medical teams and controlled chaos as the recently released medical staff, still unsure of what exactly had been going on tried to stabilise the two Atlanteans before whisking them off to the infirmary. Elizabeth wanted desperately to be with them, but the rest of her staff needed strong leadership now, and there were things here that needed taking care of.

Studiously avoiding the patch of floor that was still slippery with blood, and strewn with the torn packages, stained swabs and other detritus of immediate first aid, she stalked angrily to the remaining band of Genii intruders, who cowered back under her ferocious gaze. She strode to the nearest and said in a calm voice that fooled no-one, "If any of your leaders ever try such a thing again, then I will personally ensure that the genii are left unable to face any kind of threat for a very long time."

The miserable little band almost fell over themselves in their haste to assure her nothing like this would ever happen again, but she remained unmoved. Once their protestations had died down, she instructed them to pick up their fallen comrades, and leave, giving Ford and Bates the task of seeing them through the gate.

She stood, arms folded, watching while they picked up first Cowan, then Kolya, and started up the ramp.

"Wait!" she called. "Is Kolya still alive?"

Ford stepped up, and placed a hand over Kolya's carotid artery. He shook his head, feeling no pulse.

"Very well, carry on," she gestured to the departing Genii, who wasted no time in stepping through the gate, relieved they weren't facing being shot as well. Once the last of them had vanished into the wormhole, her control slipped slightly, and her shoulders slumped. She turned to see that Peter Grodin had the situation under control, and she nodded her approval at his handling of things. He mouthed at her to go, and she gave him a small grateful smile, hurrying out of the control room, following in Rodney's wake.

oOo

The infirmary was buzzing, staff rushing in a co-ordinated way, prepping Beckett for surgery. John was off to one side, monitors and machinery telling their own complicated story, while Rodney sat next to him, grimly watching while Carson was wheeled out. She moved over, pulled up a chair, and sat next to McKay, worriedly regarding her military commander, who still appeared to be unconscious.

McKay followed her gaze, and said expressionlessly, "The bullet went straight through the Major, and into Beckett. It's lodged in his chest somewhere, and he's bleeding. Sheppard's stable for now, so they're going to take him once they've got Carson fixed." He looked up at her. "What happened?" he asked. "One minute Sheppard seems to have everything under control, the next…everything's in a handbasket."

Elizabeth slouched down a little in the chair. It was impossible to get comfortable in the things. "I really don't know," she responded wearily. "I've sent the Genii home. Kolya and Cowan are both dead, so the only way to know will be for John to tell us. When he wakes up."

"How could someone control someone else like that? Take over and…use them? I thought you couldn't make someone do something that went against everything they are?"

Elizabeth didn't reply. She had no idea how they'd had such control over Sheppard, it would be for him to tell them what had gone on. And knowing John, he wouldn't be particularly forthcoming. In fact, she had a hunch that his physical recovery was going to be a heck of a lot easier than his psychological one.

The hours passed slowly. Weir and McKay had long ago given up trying to make conversation, and now just sat, waiting, trying to make sense of the situation, tired minds going over and over again the events that had led them to this.

Finally, Dr. Biro appeared from the surgical area, and wearily stripped off the mask she'd been wearing. Seeing the two maintaining vigil over Sheppard, she smiled, and came over.

"Carson will be fine," she said. "He came through the surgery well, the bullet wasn't too hard to remove, it had lost a lot of its momentum from going through the Major first. He'll have to have some time off which won't please him, but a few weeks should see him back in the saddle."

Elizabeth and Rodney felt at least some of their worries lifted. They watched as Dr. Biro examined Sheppard's chart, then she replaced it and said, "Now for the Major. Hopefully his should be a shorter surgery, just a matter of fixing the holes, so to speak. It's the effect the surgery will have on his other injuries that concerns me. Still, he's young, fit, and a fighter, so I don't anticipate too many problems."

She signalled to one of the other staff members, and together they wheeled John away to surgery. Almost at the same time, Carson was wheeled out, and the two shifted to sit with him, while they waited on news about Sheppard. They took in the wires, tubes and monitors that surrounded Beckett, and were surprisingly reassuring considering his pallor, and settled down to wait, Elizabeth holding the unconscious man's hand, whether for his comfort or hers she wasn't sure. It was going to be a long night.

oOo

_Several Weeks Later._

Elizabeth Weir stood at the railing on the balcony overlooking the gate. The wormhole had shut down a few minutes previously, but she was still there, a troubled frown on her face. She had just watched her second in command go through, and he was anything but the same man he'd been all those weeks previously. This time there'd been no jaunty wave, no last glance back, and no quirky little grin. Just a dogged determination to go through, and get back. His posture and body language had said it all.

He'd sat through the briefing, barely saying a word, eyes downcast, speaking to no-one unless asked a direct question. She stood straighter. This couldn't go on. She couldn't let it carry on, and now it was time for her to do something about it. Squaring her shoulders, feeling a little better, she strode off towards the infirmary, and Carson Beckett.

She found the man in question cheerfully informing one of the lab staff that he would need a course of antibiotic injections over the next week, one a day until the wound he'd sustained had healed further. And that that should be a lesson to be more careful in future. The technician slunk off, moving carefully, one hand pressed to his tender anatomy.

Elizabeth watched him go, a small smile playing across her lips.

"Why, Doctor Beckett, I believe you enjoyed that," she said in a mildly chiding tone.

"Aye, I did. And maybe next time he'll watch where he's putting his used glassware instead of Helen Morgan's..er… chest." He finished scribbling in the unfortunate young man's chart, then came over to where Dr. Weir was standing.

She watched him covertly. He seemed almost fully recovered from his ordeal, and if he moved occasionally with a certain stiffness, it didn't seem to be impeding him in any way.

"Glad to be back?" she asked. Beckett had been certified fit for duty just a few days ago.

"Oh, yes. I was going stir crazy, there's only so many journals I can read, and I was running out of places to hide from Rodney always wanting me to try and turn on Ancient technology."

She smirked, then grew more serious. "Has John been to see you?"

The smile faded from Carson's face. "No, he hasn'ae," he replied, accent thickening. "I tried to see him on a few occasions, but he always managed to avoid me. I think he's got a guilt complex the size of the Empire state building. In fact I'm sure he has."

"Do you know if he's still seeing Heightmeyer?"

"He is, but she's getting increasingly frustrated with him. There's no flies on the Major, and he knows just exactly what to say in response to her questions. She knows there's more going on with him than he lets on, but until he can be honest with her, there's little she can do."

"Well, if we can't get him to open up, I'm afraid something's going to give. He's just not…John."

There was a pause while they contemplated what was going on with their military leader. Although Carson hadn't seen him face to face, he'd seen him in the distance, and was getting reports from others about how different the man was these days. Junior military staff were frankly terrified of putting a foot wrong, and Bates and he just weren't speaking. Even Ford was keeping a distance these days. Teyla was doing her best, and now that John was physically fit again, they'd resumed their stick fighting sessions, but, Teyla said, he was too easy to beat. The spark had gone, and he was merely going through the motions. She too was at a loss for what to do to help her friend.

The pause lengthened, and Elizabeth was just about to make her apologies and leave, when their earpieces crackled into life.

"Medical team to the gateroom!"

Beckett groaned, he knew, as did Elizabeth that the only team offworld was Major Sheppard's.

Elizabeth tapped her earpiece. "What's going on?" she asked tersely, even as she headed to the nearest transporter.

"It's Major Sheppard's team, ma'am," responded the gate technician, "He's coming in hot."

"On my way," she replied, breaking into a run. "Dear God," she thought, "Couldn't the Major get a break?"

She skidded into the gateroom just in time to see the Major's team topple through the gate, and fall to lie unmoving on the gateroom floor.

TBC


	10. Chapter 10

PROTECTIVE INSTINCTS part 10

**And now...the conclusion.**

Elizabeth Weir signed the last of the current reports on her desk, and made her way to the infirmary to check on Major Sheppard's team. She had called down earlier, But Dr. Beckett had been busy, and had only time to tell her that it looked like they had all been struck by Wraith stunner blasts. She had expressed surprise, the planet they had been visiting was supposed to have been uninhabited, but Carson told her he'd check in with her later, and had signed off.

Now she had a few minutes spare, she thought she'd wander down and find out how they all were. She found Carson at his desk, busy updating the medical records of SGA1, but no sign of any of the team.

"Aye, I sent them to their quarters on strict instructions to rest," said Beckett in response to her look of surprise. "It appears they were ambushed by the Wraith and had a hard time getting back to the gate, but I'm afraid you'll have to wait for a couple of hours for your mission de-brief."

"Very well, it can wait until the stunner effects have completely worn off. Were they all ok?"

Beckett knew as well as Elizabeth she was referring indirectly to Major Sheppard.

"As well as could be expected," was the non committal reply

Thoughtfully Elizabeth made her apologies, and left to return to the ever present paperwork. She was completely taken aback to see John Sheppard standing at ease in front of her desk.

"Major Sheppard," she said, "This is a pleasant surprise. I thought you were under instructions to rest?"

As soon as he was aware of her presence, Sheppard snapped to attention. Dr Weir felt a sense of foreboding, this wasn't going to be good. The man looked brittle enough to shatter where he stood. She made her way behind the desk, and sat down in the only comfortable chair she'd so far managed to find on Atlantis.

"At ease, Major," she said, trying to lighten the atmosphere.

Sheppard stayed rigidly in place. "Dr. Weir, ma'am," he began, "I'd like to tender my resignation, effective immediately."

For a moment, Elizabeth was stunned. This was the last thing she'd been prepared for, though in hindsight, maybe she should have seen it coming. She hesitated briefly, knowing this was going to take very careful handling.

"What will you do?" she asked eventually, stalling for time.

Still not making eye contact, still looking resolutely at a spot just above her left shoulder, Sheppard replied, "I thought I'd go to the mainland and offer my services to the Athosians, with your permission, of course." So carefully formal.

"You realise you'd be giving up flying?" she was desperately stalling, trying to buy time while she thought of what to do.

A shadow passed across John's features, but he merely replied, "Yes, ma'am."

"Sit down, John," she invited, softening her voice, "And we can talk about this."

"Thank you, I'd rather stand." The voice was icily controlled. She could see this was taking a huge effort.

"Have you really thought about this?"

"Yes, ma'am."

She paused, gathering her thoughts, making him sweat, then, "I am sorry Major Sheppard, but I cannot accept your resignation at this time. Perhaps if we survive the expected invasion from the Wraith, I will reconsider, but at this time there is no-one who could take your place." She too could be icily formal.

"Lieutenant Ford could-"

"Lieutenant Ford is an excellent junior officer, and I stress, junior. He needs the example of a good commanding officer to follow if he is to achieve his full potential."

"But he and Sergeant Bates-"

Again she cut him off sharply.

"Sergeant Bates has his hands full with base security. Now is not the time for him to be trying to fill someone else's position. One which, I might add, he has had no training for. I repeat. I cannot accept your resignation at this critical time for Atlantis," (or ever, she privately thought). "If at such time after we have defeated the Wraith we can contact Stargate command, then I will consider requesting a replacement. Until then, your duties will remain as they are now. You are dismissed."

Elizabeth sat at her own version of 'attention' until Major Sheppard, still rigidly straight, marched out of her office. Only then did she allow herself to relax. She tapped her earpiece. "Dr. Beckett?" she asked, "This is Dr. Weir, please come to my office, there is something we need to discuss."

oOo

John Sheppard strode from Elizabeth's office, mind whirling. Couldn't she see? Couldn't any of them understand? He wasn't fit to do this job, never had been. He hadn't asked for it, it had been thrust upon him, and he'd shown time and time again how unworthy he was. Look at the incident with the nanobots, he could have ended up infecting everyone. Look at the whole waking the Wraith thing, look at this last god-awful mess of a mission; look at- suddenly dizzy, he stumbled into a wall, heedless of the concerned glances of other staff members in the corridor. He simply wasn't aware of them.

He stayed there for a minute, the effects of the stunner blast having obviously not entirely gone, gathering his strength, but inside, his mind was still in turmoil. He just couldn't do this anymore. Swaying dizzily, he made his way back to his quarters. He needed peace, he needed a place to think.

But once in his room, it felt confining, the walls were pressing in. If only he could relax. He couldn't remember how long ago it was since the last time he'd had a decent nights sleep. All too often he'd wake up in a cold sweat, sheets tangled as memories of his nightmare, memories of Kolya taking over, faded slowly. Every night it was the same, sleep came easily enough, but it was filled with images of himself shooting Beckett in cold blood. Or Kolya doing to Elizabeth what he had always threatened to do while he stood by, and watched, helpless. Or Cowan slowly killing Rodney by radiation poisoning as he forced him to complete their 'super-weapon'. Yeah, the last time he'd had a good nights rest was when he'd been drugged to insensibility in the infirmary.

An idea began to germinate in his mind. Drugs. Drugs helped. Oh, not those piddling sedatives Dr. Biro had given him to begin with when he'd first started having nightmares, no, they only made it worse. Trapped him in his own mind so he couldn't wake from whatever evil deed he was doing at the time. Nope, he needed the really strong ones, but they were locked securely away, and he wasn't yet at the stage where he'd hold Beckett at gunpoint, but unbidden, images flashed into his mind as to when he had done just that. Shaken, he sat heavily on his bed, distractedly running a hand through his already dishevelled hair.

So, no drugs then. What else? Alcohol. He hadn't got blind stinking drunk since he couldn't remember when, though it had happened a fair few times after Afghanistan. He was aware enough to know he was standing at the top of a very slippery slope here, but God, something had to give and soon. If he couldn't get out of Atlantis, if he couldn't get away from doing a piss-poor job of ranking military officer, something had to give. So, alcohol it was then. And he knew just where to get it. Zelenka. The man had enough gut-rot stashed to poison half of Atlantis.

Now he had a plan, some of the steely determination returned. Find Zelenka, 'persuade' him to part with a generous amount of moonshine, find somewhere to hole up and get mind-numbingly pissed. And there was the hub of it. Mind-numbing. Just for a while. Just to stop it for a little while and get some peace. Without being exactly aware he was doing it, he strapped on his 9mm, and headed out the door.

oOo

Elizabeth and Beckett were in her office, discussing what, if anything could be done to help Major Sheppard get through this. It was obvious the man wasn't coping well with what he perceived as being his inability to protect Atlantis, though privately Elizabeth felt the Major's protective instincts were what had saved them all so far.

Carson sat back in the chair opposite Elizabeth, and absently rubbed at the recently healed wound in his chest, which still ached whenever he was stressed. Like now.

He was pondering where to go next with treating the Major; he had confessed to not being completely surprised that Sheppard had tried to resign.

"What can we do?" asked Elizabeth, obviously unsettled by the recent turn of events.

"I could try a course of anti-depressants," pondered Carson aloud, "But that's really only a short-term option. And I don't see Major Sheppard being happy about taking them."

They lapsed into silence, each trying to come up with a magical solution that would magically reverse the psychological damage done to the Major, when their earpieces crackled into life.

"Elizabeth? This is Rodney, I think you need to get down to Zelenka's lab straight away."

"Why? What has happened? Is Dr. Zelenka alright?"

"Just get down here, Elizabeth, and if Carson's still with you, bring him too."

"On my way." Both quickly exited Elizabeth's office and hurriedly made their way to Zelenka's lab.

When they arrived, Rodney was leaning against a wall, watching Zelenka pace. The scientist was muttering_, "Hloupy…hloupy..az k brat tolik…proc ne spravedlivy ptatse?_

"What happened?" asked Elizabeth.

"Is Dr. Zelenka alright?" Queried Beckett, watching the man pace.

Zelenka had caught sight of them. "Yes, yes, Zelenka is alright," he said tersely. "But Major Sheppard? I think not for long."

"Dr. Zelenka, please, what happened?" asked Elizabeth.

"Major Sheppard has taken some of my…er …private supply of vodka, too much, and has gone to the ground he says. If he drinks all that, then _nemocny vule ba an ale jdete blizky…a hloupy proc JA pozadovat dotonce libit se…_ I mean, he will be very sick, and I will not be responsible.."

"Is that why you got me here, Rodney? For Major Sheppard?"

"Carson, the man is clearly not thinking straight. Of course, if you want him back in your infirmary with alcohol poisoning, then lets all leave him to it. On the other hand…"

"Ok, Ok, I get your point. We'd better find him, Elizabeth."

Dr.McKay produced a lifesigns detector. "Not that I think I'll need it," he said smugly, "I know where he usually goes if he wants to be left alone."

They found him exactly where Rodney said they would, outside on a balcony overlooking the sea, but not overlooked by anything else. As the door slid open, they could see him huddled in a corner, looking out to sea, absently swigging from the bottle held in his left hand. His right hand held his 9mm, loosely, but the fact that it was out of its holder was enough to fill Elizabeth with trepidation.

Carson evidently felt the same way as his sharply exclaimed "Major!" showed.

Major Sheppard languidly waved the hand holding the gun in their direction. Although from the looks of the empty containers beside him he'd drunk a fair amount, his voice was still clear. "Carson, Elizabeth, Rodney, come to join the party?" he held the half empty bottle up as if he was giving a toast, then took another drink.

"Major," said Carson calmly, "I think you've had enough, lad."

"No, I haven't," came the clear response. "Not nearly enough. Want some? Though you'll have to get your own, this is for me."

Elizabeth spoke up. "John, come inside. Put down the gun, and come on in. We're here to help, if you'll let us."

Sheppard gave a small, humourless laugh, then stood, swaying slightly. "Help?" he said, "How? What're you gonna do? Turn time back? Bring Sumner back from the dead?" He took another drink, watching them from the corner of his eye.

"Honestly," said Elizabeth, "I don't know. But drowning your woes in bad alcohol isn't going to help."

Sudden fury blazed in Sheppard's eyes, and Elizabeth took an involuntary step back. "How would you know?" he asked hissing out the question in alcohol fuelled rage. "Do you see Carson, Rodney, you, Hell, everybody dying every time you close your eyes because you weren't able to stop it? Do you? Do you know what it felt like to pull a gun on your friend and get ready to shoot him, and know you were going to do it, despite the fact you were screaming inside to stop? No? Then how do you know getting out of my mind drunk isn't going to help?" He turned, and looked out to sea, temporarily ignoring them.

Carson moved forwards to put a hand on Sheppard's shoulder in a gesture of support. Sheppard swung round faster than Beckett could have thought possible considering how much drink the man had in him, and brought the gun up, waving it in Beckett's general direction unsteadily. No-one said a thing, the silence heavy as Sheppard came to realise what he had just done. He dropped the gun as if it was red hot, and regarded Beckett with stricken eyes.

"God! Carson, I'm sorry, I'm sorry, I just- I just can't stop it. It plays over and over again, and most times I end up shooting you! I'm just-its just-" he wavered, and sank to the floor, pulling himself into a corner as tightly as he could, wrapping his arms around his legs, as if trying to hold himself together, which maybe he was. Carson knelt down beside him, kicking the gun towards Elizabeth and Rodney, out of harms way.

"Its alright, lad," he said gently, pulling the Major towards him in a comforting hug. "No-one here holds anything against you, you weren't in control of yourself at the time."

And then, as if a damn had burst, it all came out, all the fear and uncertainties, the indignity, the treatment he'd received at the hands of the Suventans, the feeling as if he was losing his mind, his self and not being able to do a thing to stop it, or control it, having everything that made him John Sheppard shredded, torn and taken away from him.

In a halting voice, under Carson's gentle prompting, he told them the story of what had gone on, what he'd been through. He told them of the cold water tank, the hot room, the beatings. He told them of how he'd thought they were going to operate on him while he was awake. He told them about fighting off the amorous attentions of a prison guard, and how afterwards all the guards 'friends' had come and taken their frustrations out on him with their fists. He ignored the horrified glances each was giving the other, took a fortifying drink, and carried on. He told them of how Kolya had 'visited' several times, and had spent a while listing everything he was going to have Sheppard do once he was under genii control. His voice wavered several times, but he carried on relentlessly, telling them of how Councillor Jaq'an had shown him off to visitors from other planets, as if he was a prize piece of beef, the sleep deprivation, lack of food, drugged water, and being denied the basics of daily living, the humiliation of having to perform his most basic functions in front of an audience, how they had tried to strip away his basic humanity, of having Kolya in his head all the fucking time. His voice, monotone through the whole appalling tale gradually faltered to a halt.

Rodney and Elizabeth stood well back, and let the words wash over them with a sense of horror. They had no idea it had been so bad. And finally when it was all out, and Sheppard, the strongest man they knew sat holding onto Beckett like a lost and lonely child, they finally understood.

oOo

A few hours later, Carson came to Ford, Teyla, Rodney and Elizabeth as they waited just outside the infirmary for news of the Major. His face was more relaxed than it had been for a while. He took in their questioning faces, and allowed himself a relieved smile.

"He's sleeping like a baby, though I've no doubt he's going to wish he'd never heard of Zelenka's brew when he wakes up."

"Will he be ok?" asked Rodney worriedly. It had shaken him to see the Major lose it like that.

"Well, it's not going to be an easy road, and he's going to need some space, and understanding from all of us, but yes, given time I think he'll be back to his old self."

"Then we must make him understand that he does not have to be alone," said Teyla pragmatically. "Are we allowed to visit?"

"Aye, for a few minutes, but mind, no waking him up. I suspect this is the first time he's slept this peacefully in a long time."

Sheppard's team quietly entered the infirmary, feeling more hopeful than they had for a while.

oOo

EPILOGUE

The warning klaxons sounded, and the wormhole whooshed into life. Elizabeth Weir stood at the balcony, her posture reflecting a calm she didn't feel. This was the first time Major Sheppard's team had gone through the gate since his…well since his breakdown. And now they were due back, and miracle of miracles, they were on time.

She watched, feeling a weight lift from her shoulders as they stepped through, Rodney and the Major arguing good-naturedly about something, while Teyla and Ford looked on in a long suffering manner. Sheppard caught sight of her, and smiled up at her, and she knew that things were just about back to normal.

THE END

And thats it. I hope I got the Czech right.


End file.
